Strain identifier

BacDive ID: 6420

Type strain: Yes

Species: Ligilactobacillus aviarius

Strain Designation: 75

Strain history: CIP <- 1988, DSM <- T. Mitsuoka: strain 75

NCBI tax ID(s): 1606 (species)

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General

@ref: 8875

BacDive-ID: 6420

DSM-Number: 20655

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-positive

description: Ligilactobacillus aviarius 75 is an anaerobe, Gram-positive bacterium that was isolated from faeces of chicken.

NCBI tax id

  • NCBI tax id: 1606
  • Matching level: species

strain history

@refhistory
8875<- T. Mitsuoka, 75
67770T. Fujisawa 75.
116662CIP <- 1988, DSM <- T. Mitsuoka: strain 75

doi: 10.13145/bacdive6420.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Ligilactobacillus
  • species: Ligilactobacillus aviarius
  • full scientific name: Ligilactobacillus aviarius (Fujisawa et al. 1985) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus aviarius

@ref: 8875

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus aviarius

full scientific name: Ligilactobacillus aviarius (Fujisawa et al. 1985) Zheng et al. 2020

strain designation: 75

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 92.909

colony morphology

  • @ref: 50913
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8875BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water
8875MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)yeshttps://mediadive.dsmz.de/medium/232Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)2 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
35492MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminisyesDistilled water make up to (900.000 ml);Man Rogosa Sharp broth (55.000 g);Cysteine hydrochloride 5 % solution - M0172 (100.000 ml)
116662CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperature
8875positivegrowth37
35492positivegrowth37
50913positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8875anaerobe
50913anaerobe

spore formation

@refspore formationconfidence
69480no93.419
69481no100

murein

  • @ref: 8875
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose-builds acid from15824
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8875-----------+-+/------------+/---+---------------------
116662-------------------------------------------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8875----------+------+--++-++-+/--+/-

Isolation, sampling and environmental information

isolation

@refsample type
8875faeces of chicken
50913Chicken feces
67770Chicken feces
116662Animal, Chicken, feces

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4454.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_2227;97_2697;98_3347;99_4454&stattab=map
  • Last taxonomy: Ligilactobacillus
  • 16S sequence: LC071825
  • Sequence Identity:
  • Total samples: 26439
  • soil counts: 1429
  • aquatic counts: 1732
  • animal counts: 22696
  • plant counts: 582

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88751Risk group (German classification)
1166621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus aviarius strain DSM 20655 16S ribosomal RNA gene, partial sequenceM588081504nuccore1606
20218Ligilactobacillus aviarius JCM 5666 gene for 16S rRNA, partial sequenceAB289044691nuccore147810
20218Ligilactobacillus aviarius NBRC 102162 gene for 16S rRNA, partial sequenceAB3263551488nuccore147810
67770Ligilactobacillus aviarius JCM 5666 gene for 16S ribosomal RNA, partial sequenceLC0718251455nuccore1606

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus aviarius subsp. aviarius DSM 206551423821.4wgspatric1423821
66792Lactobacillus aviarius subsp. aviarius strain NBRC 102162147810.5wgspatric1606
66792Ligilactobacillus aviarius aviarius DSM 206552700989116draftimg1423821
67770Ligilactobacillus aviarius subsp. aviarius DSM 20655GCA_001436315scaffoldncbi1423821
67770Ligilactobacillus aviarius NBRC 102162GCA_007989665contigncbi1606

GC content

@refGC-contentmethod
887538.7
6777040.1genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.909no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no57.724yes
69480spore-formingspore-formingAbility to form endo- or exosporesno93.419no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.375yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno89no

External links

@ref: 8875

culture collection no.: DSM 20655, ATCC 43234, CCUG 32230, JCM 5666, BCRC 14048, CIP 103144, KCTC 5063, LMG 10753, NBRC 102162, NCFB 2786, NCIMB 702786

straininfo link

  • @ref: 75895
  • straininfo: 125561

literature

  • topic: Metabolism
  • Pubmed-ID: 29502827
  • title: Biochemical characterization of two GH70 family 4,6-alpha-glucanotransferases with distinct product specificity from Lactobacillus aviarius subsp. aviarius DSM 20655.
  • authors: Meng X, Gangoiti J, de Kok N, van Leeuwen SS, Pijning T, Dijkhuizen L
  • journal: Food Chem
  • DOI: 10.1016/j.foodchem.2018.01.154
  • year: 2018
  • mesh: Amino Acid Motifs, Amylose/chemistry/metabolism, Biocatalysis, Dietary Fiber, Digestion, Glucans/chemistry/metabolism, Glycogen Debranching Enzyme System/*chemistry/*metabolism, Lactobacillus/*enzymology, Substrate Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8875Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20655)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20655
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35492Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14909
50913Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32230)https://www.ccug.se/strain?id=32230
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75895Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125561.1StrainInfo: A central database for resolving microbial strain identifiers
116662Curators of the CIPCollection of Institut Pasteur (CIP 103144)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103144